Phylogeographic patterning of mtDNA in the widely distributed harvest mouse (Micromys minutus) suggests dramatic cycles of range contraction and expansion during the mid- to late Pleistocene

Abstract

Abstract:We examined sequence variation in the mitochondrial cytochrome b gene (1140 bp, n = 73) and control region (842-851 bp, n = 74) in the Eurasian harvest mouse (Micromys minutus (Pallas, 1771)), with samples drawn from across its range, from Western Europe to Japan. Phylogeographic analyses revealed region-specific haplotype groupings combined with overall low levels of inter-regional genetic divergence. Despite the enormous intervening distance, European and East Asian samples showed a net nucleotide divergence of only 0.36%. Based on an evolutionary rate for the cytochrome b gene of 2.4%·(site·lineage·million years) -1 , the initial divergence time of these populations is estimated at around 80 000 years before present. Our findings are consistent with available fossil evidence that has recorded repeated cycles of extinction and recolonization of Europe by M. minutus through the Quaternary. The molecular data further suggest that recolonization occurred from refugia in the Central to East Asian region. Japanese haplotypes of M. minutus, with the exception of those from Tsushima Is., show limited nucleotide diversity (0.15%) compared with those found on the adjacent Korean Peninsula. This finding suggests recent colonization of the Japanese Archipelago, probably around the last glacial period, followed by rapid population growth.Résumé : Nous avons étudié la variation des séquences du gène mitochondrial du cytochrome b (1140 pb, n = 73) et de la région de contrôle (842-851 pb, n = 74) dans des échantillons de rats des moissons (Micromys minutus (Pallas, 1771)) répartis sur toute l'aire de répartition, de l'Europe de l'Ouest jusqu'au Japon. Des analyses phylogéographiques révèlent l'existence de regroupements régionaux d'haplotypes, ainsi que des niveaux globaux faibles de divergence gé-nétique entre les régions. Malgré les distances considérables entre eux, les échantillons de l'Europe et de l'Asie de l'Est possèdent une divergence nette des nucléotides de seulement 0,36 %. Avec un taux d'évolution du gène du cytochrome b de 2,4 %·(site·lignée·million d'années) -1 , la divergence initiale estimée de ces populations se situe à il y a environ 80 000 années. Nos résultats concordent avec les données disponibles sur les fossiles qui indiquent des cycles répétés d'extinction et de recolonisation de M. minutus en Europe durant le quaternaire. Les données moléculaires laissent aussi croire que la recolonisation s'est faite à partir de refuges des régions centrales et orientales de l'Asie. Les haplotypes de M. minutus du Japon ont une faible diversité des nucléotides (0,15 %), à l'exception de ceux des îles Tsushima, par comparaison à ce qui prévaut dans la péninsule adjacente de Corée. Cette information laisse croire à une colonisation récente de l'archipel japonais, probablement aux environs de la dernière période glaciaire, suivie d'une croissance rapide des populations.[Traduit par la Rédaction] Yasuda et al. 1420

Evolutionary and dispersal history of Eurasian house mice Mus musculus clarified by more extensive geographic sampling of mitochondrial DNA

“…The PCR and direct sequencing of the CR (around 800 bp; Yasuda et al, 2005) and Cytb (1140 bp; Suzuki et al, 2004) were performed according to previously described methods. Two primers were used for sequence determination of CR in M. musculus; CR1: 5 0 -CATGCCTTGACGGCTATGTT-3 0 and CR2: 5 0 -ATC GCCCATACGTTCCCCTT-3 0 .…”

The origin of Swedish and Norwegian populations of the Eurasian harvest mouse (Micromys minutus)

“…We also obtained published sequences from other areas in Europe (Yasuda et al 2005; GenBank accession numbers: AB125095, AB125097-AB125100, AB201981-AB201983, AB201975 and AB201976 for cytb, and AB202039.1, AB202040.1 and AB202048.1-AB202057.1 for the ctrl region). Museum specimens from Denmark had been stored in formalin, so DNA from these were extracted with QIAamp DNA FFPE tissue kit (Qiagen GmbH, Germany); using this method, we were able to amplify both cyt b and control region sequences from four out of six available specimens.…”

“…DNA from all other samples was extracted by placing biopsies in lysis buffer and proteinase K, where after the DNA was precipitated in ethanol, as described in Laird et al (1991). We amplified 1,140 bp of the cytochrome b region and 842 bp of the ctrl region using the primers and PCR conditions described by Yasuda et al (2005). PCR products were sequenced in both directions using ABI Prism Big Dye Terminator Cycle Sequencing Ready Reaction Kit on an ABI 3100 sequencer (Applied Biosystems).…”

“…The models were chosen using MrModeltest v2 separately for each of the genes (Nylander 2004). Trees were rooted using ctrl and cyt b from the specimens collected in Russia (Yasuda et al 2005). …”

Variation in the Coat-Color-Controlling Genes,Mc1randAsip, in the House MouseMus musculusfrom Madagascar

“…Polymerase chain reaction (PCR) and direct sequencing of the mitochondrial control region (CR, ~800 bp) and Cytb (1,140 bp) were performed according to previously described methods (Suzuki et al 2004Yasuda et al 2005). The entire coding region of the Mc1r gene (948 bp; 316 codons including a stop codon) was sequenced using the primer sets developed by Shimada et al (2009).…”